Evidences of the present of the promoter like elements into the non-coding regions of the human coagulation factor VIII gene
سال
: 2016
چکیده: Accurate prediction of the Cis-regulatory elements encoded within DNA sequences
throughout the genomes and in different regions of a gene is a crucial step towards
understanding the regulatory mechanism of the gene expression. Bearing in mind, the
complete sequences of the human coagulation factor VIII (hFVIII) gene were investigated to
identify and characterize promoteric like sequences (PLS) based on in-silico examination. In
this regard, the sequences of the hFVIII gene as well as protein sequence of the human RNA
polymerase II (RNAPII) retrieved from Genebank and PDB with accession number
AY769950 and 2F3I, respectively. Subsequently presence of any promoter areas throughout
the gene was investigated based on potential transcription start positions by linear
discriminant function combining characteristics describing functional motifs and
oligonucleotide composition of these sites using FPROM program and evaluated via Cluspro
and PatchDock programs and also visualized with Pymol software. Our analysis led to
revealed 43 regions, containing enhancer-like elements and promoter-like elements
throughout the hFVIII gene except in the introns 8, 11, 12, 16-20 in four groups including
really, intronic, exonic and pseudo promoters that are located in the 5'UTR, intronic regions,
exonic regions and 3'UTR, respectively with independent of the intron length. Moreover,
assessment the binding affinity of these regions to RNAPII showed suitable connection and
level of energy even less than really promoter in some case of intronic promoters. Altogether,
the data obtained in this study has provided further proofs for potentials of the intronic regions
for regulatory functions as well as promoteric regions with high affinity to RNAPII for
application as self-promoter in new vector designing. However, experimental analysis of the
detected regions to examine their potential regulatory functions on a reporter gene is the next
step to this work.
throughout the genomes and in different regions of a gene is a crucial step towards
understanding the regulatory mechanism of the gene expression. Bearing in mind, the
complete sequences of the human coagulation factor VIII (hFVIII) gene were investigated to
identify and characterize promoteric like sequences (PLS) based on in-silico examination. In
this regard, the sequences of the hFVIII gene as well as protein sequence of the human RNA
polymerase II (RNAPII) retrieved from Genebank and PDB with accession number
AY769950 and 2F3I, respectively. Subsequently presence of any promoter areas throughout
the gene was investigated based on potential transcription start positions by linear
discriminant function combining characteristics describing functional motifs and
oligonucleotide composition of these sites using FPROM program and evaluated via Cluspro
and PatchDock programs and also visualized with Pymol software. Our analysis led to
revealed 43 regions, containing enhancer-like elements and promoter-like elements
throughout the hFVIII gene except in the introns 8, 11, 12, 16-20 in four groups including
really, intronic, exonic and pseudo promoters that are located in the 5'UTR, intronic regions,
exonic regions and 3'UTR, respectively with independent of the intron length. Moreover,
assessment the binding affinity of these regions to RNAPII showed suitable connection and
level of energy even less than really promoter in some case of intronic promoters. Altogether,
the data obtained in this study has provided further proofs for potentials of the intronic regions
for regulatory functions as well as promoteric regions with high affinity to RNAPII for
application as self-promoter in new vector designing. However, experimental analysis of the
detected regions to examine their potential regulatory functions on a reporter gene is the next
step to this work.
کلیدواژه(گان): hFVIII,Gene expression,Cis-regulatory elements,promoter,in-silico biology
کالکشن
:
-
آمار بازدید
Evidences of the present of the promoter like elements into the non-coding regions of the human coagulation factor VIII gene
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| contributor author | علی اکبر حداد مشهد ریزه | en |
| contributor author | Aliakbar Haddad-Mashadrizeh | fa |
| date accessioned | 2020-06-06T14:24:10Z | |
| date available | 2020-06-06T14:24:10Z | |
| date copyright | 3/6/2016 | |
| date issued | 2016 | |
| identifier uri | http://libsearch.um.ac.ir:80/fum/handle/fum/3395167 | |
| description abstract | Accurate prediction of the Cis-regulatory elements encoded within DNA sequences throughout the genomes and in different regions of a gene is a crucial step towards understanding the regulatory mechanism of the gene expression. Bearing in mind, the complete sequences of the human coagulation factor VIII (hFVIII) gene were investigated to identify and characterize promoteric like sequences (PLS) based on in-silico examination. In this regard, the sequences of the hFVIII gene as well as protein sequence of the human RNA polymerase II (RNAPII) retrieved from Genebank and PDB with accession number AY769950 and 2F3I, respectively. Subsequently presence of any promoter areas throughout the gene was investigated based on potential transcription start positions by linear discriminant function combining characteristics describing functional motifs and oligonucleotide composition of these sites using FPROM program and evaluated via Cluspro and PatchDock programs and also visualized with Pymol software. Our analysis led to revealed 43 regions, containing enhancer-like elements and promoter-like elements throughout the hFVIII gene except in the introns 8, 11, 12, 16-20 in four groups including really, intronic, exonic and pseudo promoters that are located in the 5'UTR, intronic regions, exonic regions and 3'UTR, respectively with independent of the intron length. Moreover, assessment the binding affinity of these regions to RNAPII showed suitable connection and level of energy even less than really promoter in some case of intronic promoters. Altogether, the data obtained in this study has provided further proofs for potentials of the intronic regions for regulatory functions as well as promoteric regions with high affinity to RNAPII for application as self-promoter in new vector designing. However, experimental analysis of the detected regions to examine their potential regulatory functions on a reporter gene is the next step to this work. | en |
| language | English | |
| title | Evidences of the present of the promoter like elements into the non-coding regions of the human coagulation factor VIII gene | en |
| type | Conference Paper | |
| contenttype | External Fulltext | |
| subject keywords | hFVIII | en |
| subject keywords | Gene expression | en |
| subject keywords | Cis-regulatory elements | en |
| subject keywords | promoter | en |
| subject keywords | in-silico biology | en |
| identifier link | https://profdoc.um.ac.ir/paper-abstract-1060734.html | |
| conference title | اولین همایش شیمی زیست فناوری | fa |
| conference location | تهران | fa |
| identifier articleid | 1060734 |